Shady A. Amin

Microbial interactions are likely as old as life itself and will continue to play an integral role in shaping microbial diversity. Can we use a combination of culturing and molecular techniques (e.g. next-gen sequencing) to understand how these interactions evolved, how important are they today, and how will they respond to climate change?

Education:
Ph.D. in Bioinorganic Chemistry, University of California, San Diego/San Diego State University (2010)
M.A. in Inorganic Chemistry, San Diego State University (2005)
B.Sc. in Biochemistry, University of California, Santa Barbara (2003)

Research Interests:
I'm interested in how marine microbes talk to each other. These types of interactions are mostly uncharacterized yet they play a critical role in the physiology of interacting organisms, which leads to a change in the chemical environment surrounding those cells and subsequently to the whole ecosystem. Because diatoms are among the most important primary producers in the oceans, I am investigating inter-species interactions between diatoms (photosynthetic eukaryotes) and the two other domains of life (heterotrophic prokaryotes): 1) bacteria and 2) archaea.

1) Diatom-bacterial interactions are common in the oceans and can be beneficial or lethal. Only a small number of these interactions have been described. One possible mechanism for a diatom to detect and respond to beneficial or "pathogenic" bacteria is through detection of a molecule the bacteria produce. Many marine bacteria use hydrophobic signals to communicate with each other (i.e. quorum sensing). Similar to some plants, diatoms maybe able to detect beneficial vs lethal bacteria by differentiating between their excreted molecular signals. Currently, I'm using whole transcriptome analysis and metabolomics to study interactions between diatoms and their bacterial microflora. So far, evidence suggests there are an array of complex interactions that take place between the diatom and its many bacterial partners. (Fig. 1: Diatom-associated bacteria are confined to two phyla and a limited number of genera as illustrated by the maximum likelihood phylogenetic tree of the bacterial domain.

2) Archaea have been typically associated with extreme environments such as hydrothermal vents. However, we now know that marine archaea dominate many parts of the marine environment and influence global biogeochemical cycles. For example, Ammonia-oxidizing Archaea (AOA) play an important role in the nitrogen cycle by oxidizing ammonia to nitrite. Their dominance in many marine habitats and presence in the upper water column (e.g. chlorophyll a maxima where phytoplankton thrive) suggest that they are likely to interact with other microbes including diatoms. Currently, I'm studying trace metal limitation of the only cultured marine AOA isolate with wider implications to diatom metal availability. Recently published results from this study show that AOA may be strongly limited by Cu availability in many parts of the marine environment. Many oceanic diatoms also require a high Cu demand, suggesting that both taxa may be interacting/competing for Cu particularly in the open ocean.

(Fig. 2: This figure shows the effect of free cupric ion concentrations on ammonia oxidation of the only representative marine AOA available in culture. Based on this data, AOA are expected to be Cu-limited below 10-13 M. This value is in excess of free cupric ion concentrations measured in many parts of the oceans.